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        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

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        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.25.2

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-11-21, 11:25 EST based on data in: /gpfs/projects/GenomicsCore/BGE510

        General Statistics

        Showing 0/18 rows and 10/17 columns.
        Sample NameDuplication% AlignedM AlignedLibrary typesTotal readsAlignedAlignedUniq alignedUniq alignedMultimapped% Duplication% > Q30Mb Q30 basesReads After FilteringGC content% PF% Adapter
        SRR5448113
        7.7%
        100.0%
        4.2M
        		IU
        4.8M
        4.7M
        98.0%
        4.3M
        87.9%
        0.5M
        SRR5448113_STARpass1
        4.8M
        4.7M
        97.9%
        4.3M
        88.0%
        0.5M
        SRR5448113_subsample_1
        4.5%
        97.9%
        479.2Mb
        9.7M
        50.3%
        96.7%
        0.2%
        SRR5448114
        6.6%
        100.0%
        4.3M
        		IU
        4.8M
        4.7M
        97.9%
        4.3M
        88.5%
        0.5M
        SRR5448114_STARpass1
        4.8M
        4.7M
        97.9%
        4.3M
        88.5%
        0.5M
        SRR5448114_subsample_1
        3.8%
        97.8%
        479.3Mb
        9.7M
        50.4%
        96.7%
        0.2%
        SRR5448115
        7.9%
        100.0%
        4.2M
        		IU
        4.8M
        4.7M
        97.9%
        4.2M
        87.8%
        0.5M
        SRR5448115_STARpass1
        4.8M
        4.7M
        97.9%
        4.3M
        87.8%
        0.5M
        SRR5448115_subsample_1
        4.7%
        97.9%
        479.6Mb
        9.7M
        50.3%
        96.8%
        0.2%
        SRR5448116
        7.2%
        100.0%
        4.3M
        		IU
        4.8M
        4.7M
        98.0%
        4.3M
        88.8%
        0.4M
        SRR5448116_STARpass1
        4.8M
        4.7M
        98.0%
        4.3M
        88.8%
        0.4M
        SRR5448116_subsample_1
        4.2%
        97.9%
        478.5Mb
        9.7M
        50.5%
        96.6%
        0.2%
        SRR5448117
        7.5%
        100.0%
        4.2M
        		IU
        4.8M
        4.7M
        97.8%
        4.3M
        88.2%
        0.5M
        SRR5448117_STARpass1
        4.8M
        4.7M
        97.8%
        4.3M
        88.2%
        0.5M
        SRR5448117_subsample_1
        4.5%
        97.8%
        477.2Mb
        9.6M
        50.3%
        96.4%
        0.2%
        SRR5448118
        7.0%
        100.0%
        4.3M
        		IU
        4.8M
        4.7M
        97.7%
        4.3M
        88.4%
        0.4M
        SRR5448118_STARpass1
        4.8M
        4.7M
        97.7%
        4.3M
        88.5%
        0.4M
        SRR5448118_subsample_1
        4.2%
        97.8%
        478.6Mb
        9.7M
        50.6%
        96.6%
        0.2%

        Picard

        Tools for manipulating high-throughput sequencing data.URL: http://broadinstitute.github.io/picard

        Mark Duplicates

        Number of reads, categorised by duplication state. Pair counts are doubled - see help text for details.

        The table in the Picard metrics file contains some columns referring read pairs and some referring to single reads.

        To make the numbers in this plot sum correctly, values referring to pairs are doubled according to the scheme below:

        • READS_IN_DUPLICATE_PAIRS = 2 * READ_PAIR_DUPLICATES
        • READS_IN_UNIQUE_PAIRS = 2 * (READ_PAIRS_EXAMINED - READ_PAIR_DUPLICATES)
        • READS_IN_UNIQUE_UNPAIRED = UNPAIRED_READS_EXAMINED - UNPAIRED_READ_DUPLICATES
        • READS_IN_DUPLICATE_PAIRS_OPTICAL = 2 * READ_PAIR_OPTICAL_DUPLICATES
        • READS_IN_DUPLICATE_PAIRS_NONOPTICAL = READS_IN_DUPLICATE_PAIRS - READS_IN_DUPLICATE_PAIRS_OPTICAL
        • READS_IN_DUPLICATE_UNPAIRED = UNPAIRED_READ_DUPLICATES
        • READS_UNMAPPED = UNMAPPED_READS
        Created with MultiQC

        Salmon

        Version: 1.10.2

        Quantifies expression of transcripts using RNA-seq data.URL: https://combine-lab.github.io/salmonDOI: 10.1038/nmeth.4197

        Created with MultiQC

        STAR

        Universal RNA-seq aligner.URL: https://github.com/alexdobin/STARDOI: 10.1093/bioinformatics/bts635

        Summary Statistics

        Summary statistics from the STAR alignment

        Showing 0/12 rows and 10/19 columns.
        Sample NameTotal readsAlignedAlignedUniq alignedUniq alignedMultimappedAvg. read lenAvg. mapped lenSplicesAnnotated splicesGT/AG splicesGC/AG splicesAT/AC splicesNon-canonical splicesMismatch rateDel rateDel lenIns rateIns len
        SRR5448113
        4.8M
        4.7M
        98.0%
        4.3M
        87.9%
        0.5M
        101.0bp
        101.0bp
        1.7M
        1.7M
        1.7M
        0.0M
        0.0M
        0.0M
        0.1%
        0.0%
        1.5bp
        0.0%
        1.3bp
        SRR5448113_STARpass1
        4.8M
        4.7M
        97.9%
        4.3M
        88.0%
        0.5M
        101.0bp
        101.0bp
        1.7M
        1.7M
        1.7M
        0.0M
        0.0M
        0.0M
        0.1%
        0.0%
        1.5bp
        0.0%
        1.3bp
        SRR5448114
        4.8M
        4.7M
        97.9%
        4.3M
        88.5%
        0.5M
        101.0bp
        101.0bp
        1.7M
        1.7M
        1.7M
        0.0M
        0.0M
        0.0M
        0.1%
        0.0%
        1.5bp
        0.0%
        1.3bp
        SRR5448114_STARpass1
        4.8M
        4.7M
        97.9%
        4.3M
        88.5%
        0.5M
        101.0bp
        101.0bp
        1.7M
        1.7M
        1.7M
        0.0M
        0.0M
        0.0M
        0.1%
        0.0%
        1.5bp
        0.0%
        1.3bp
        SRR5448115
        4.8M
        4.7M
        97.9%
        4.2M
        87.8%
        0.5M
        101.0bp
        101.0bp
        1.7M
        1.7M
        1.7M
        0.0M
        0.0M
        0.0M
        0.1%
        0.0%
        1.5bp
        0.0%
        1.3bp
        SRR5448115_STARpass1
        4.8M
        4.7M
        97.9%
        4.3M
        87.8%
        0.5M
        101.0bp
        101.0bp
        1.7M
        1.7M
        1.7M
        0.0M
        0.0M
        0.0M
        0.1%
        0.0%
        1.5bp
        0.0%
        1.3bp
        SRR5448116
        4.8M
        4.7M
        98.0%
        4.3M
        88.8%
        0.4M
        101.0bp
        101.0bp
        1.8M
        1.8M
        1.8M
        0.0M
        0.0M
        0.0M
        0.1%
        0.0%
        1.5bp
        0.0%
        1.2bp
        SRR5448116_STARpass1
        4.8M
        4.7M
        98.0%
        4.3M
        88.8%
        0.4M
        101.0bp
        101.0bp
        1.8M
        1.8M
        1.8M
        0.0M
        0.0M
        0.0M
        0.1%
        0.0%
        1.5bp
        0.0%
        1.2bp
        SRR5448117
        4.8M
        4.7M
        97.8%
        4.3M
        88.2%
        0.5M
        101.0bp
        100.9bp
        1.7M
        1.7M
        1.7M
        0.0M
        0.0M
        0.0M
        0.1%
        0.0%
        1.5bp
        0.0%
        1.3bp
        SRR5448117_STARpass1
        4.8M
        4.7M
        97.8%
        4.3M
        88.2%
        0.5M
        101.0bp
        100.9bp
        1.7M
        1.7M
        1.7M
        0.0M
        0.0M
        0.0M
        0.1%
        0.0%
        1.5bp
        0.0%
        1.3bp
        SRR5448118
        4.8M
        4.7M
        97.7%
        4.3M
        88.4%
        0.4M
        101.0bp
        101.0bp
        1.8M
        1.8M
        1.8M
        0.0M
        0.0M
        0.0M
        0.1%
        0.0%
        1.6bp
        0.0%
        1.3bp
        SRR5448118_STARpass1
        4.8M
        4.7M
        97.7%
        4.3M
        88.5%
        0.4M
        101.0bp
        101.0bp
        1.8M
        1.8M
        1.8M
        0.0M
        0.0M
        0.0M
        0.1%
        0.0%
        1.6bp
        0.0%
        1.3bp

        Alignment Scores

        Created with MultiQC

        fastp

        Version: 0.23.4

        All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560

        Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

        Filtered Reads

        Filtering statistics of sampled reads.

        Created with MultiQC

        Insert Sizes

        Insert size estimation of sampled reads.

        Created with MultiQC

        Sequence Quality

        Average sequencing quality over each base of all reads.

        Created with MultiQC

        GC Content

        Average GC content over each base of all reads.

        Created with MultiQC

        N content

        Average N content over each base of all reads.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        Salmon1.10.2
        fastp0.23.4

        MultiQC v1.25.2 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.